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An active debate has been underway on the magnitude and duration of carbon (C) emissions from hydroelectric reservoirs, yet little attention has been paid to stochastic C emissions from reservoir sediments during extreme climatic events. A rare opportunity for field measurements of CO₂ efflux from a hydroelectric reservoir in Korea during an extreme drought event was used to examine how prolonged droughts can affect microbial organic matter processing and the release of CO₂, CH₄ and N₂O from exposed sediments. Chamber measurements of CO₂ efflux along an exposed sediment transect, combined with high-frequency continuous sensor measurements of the partial pressure of CO₂ (pCO₂) in the reservoir surface water, exhibited extraordinary pulses of CO₂ from exposed sediments and the turbulent inflowing water in contrast to a small CO₂ sink in the main water body of the reservoir and a low efflux of CO₂ from the flooded sediment. Significant increases in the production of CO₂, CH₄ and N₂O observed in a laboratory incubation of sediments, together with enhanced activities of phenol oxidase and three hydrolases, indicate a temporary activation of microbial organic matter processing in the drying sediment. The results suggest that drought-triggered pulses of greenhouse gas emission from exposed sediments can offset the C accumulation in reservoir sediments over time scales of years to decades, reversing the trend of declining C emissions from aging reservoirs.